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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG

Basic information

species Arabidopsis thaliana
transcript AT5G22770.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 7
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaat--ttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
|| | |  ||||| | |  |  | | || |  |  | |   ||  |      |  |||  | ||||  | |   |  |||||||  | ||||| || |||||||| || |||||||| |||||||| || || |||||||| || |||||||| || |||||||||||  | |||
gtactaccttttctttta-acttttctagtgcacctgtacaaaaatgtgtggactgcaatg-attttgttgttgtccttcagGTTTTACAGCGTATTTTGATGGGTACTGATGTTGTTAAAAATGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTG

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 8
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
    | ||  ||  | |     |||     |  |||  |  ||| |       |   |||  |||      |   |||||||  | ||||| || |||||||| || |||||||| ||||| || || || |||||||| || |||||||| || |||||||||||  | |||
--gtactacctttttttacttctctactgaacctgtactaaaatgtgtggat-tataatgatattattgtcatccttcagGTTTTACAGCGCATTTTGATGGGTACTGATGTTGTTAAAAACGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTG

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 7
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
|||   || | |||  |  | |  |  || |  | |||||   |  |   |  | |    || ||   |    |||||||||| | ||  | ||| ||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || |||||||| ||  | |||
gtttg-taatatcaaattgacacatccaaaaactttctttagttaacaaattttagtg-agccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGAACTGATGTTGTGAAAAATGTGAACAAAAATAATGCATCCCATGCTGTTCTTTTTGAAGCCCTTGCTCTG

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
|||   || | |||  |  | |  |  || | |        | ||  |     |      || ||   |    |||||||||| | ||  | ||| |||||||||| |||||||| ||||||||||| ||||| ||||| || ||||| || || |||||||||||  | |||
gtttg-taatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 7
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
|| |   ||||    | | | || | | | ||     |  || |||    |  |         | |   |    |||||||| || || || ||||| ||||| || |||||||||||||| ||||| || |||||||| || |||||||| ||||||||||| ||  | || 
gtactccatttctcagcgaatatatttca-attctcatcagattttgtaattctaatgaaatctgttgggtggttttcagGTTCTACAACGGATATTAATGGGAACTGATGTTGTGAAAAACGTGAACAAGAACAATGCCTCACATGCTGTTCTGTTTGAAGCCCTTGCTCTT

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S171_160V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
                       | |  || ||       ||  |  ||| |  |  | || || | ||||| |     ||     |||  | |   |  ||||| || ||   ||| ||| || | |||||||||||||||||  | |||||||||||||| ||||||||||| || ||||| || || ||  ||
ctctgcgtcacgttttgggtagaggtttatgttagttacagtttaaatgtgac-tgcgcctctgtaattcct-taggatcacaaatttttcttgctgtg-cagGTTCTACAAACAATCTTGTTGCGTACAGATGTTGTGAAAAACATTAATAAAAACAATGCATCTCATGCTGTTCTCTTTGAGGCACTTTCTTTG

upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------gttcaatattt-----tcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
                     || |||   |     || | | | |   |   |||  | || ||  ||    |   || ||   |  || | |     ||  ||    | ||||| || ||| |||| || |||||||| || ||||| |||||||||||||| || ||||| || || |||||||| ||  | |||
cactatttacatccaaatgtattgaattactgaggatcctat-tgatgtttccatacttatccttttatccttttctattgcgacgtgttacgtt----ttgtagACTTTGCAGCGCATTTTGTTGGGAACTGATGTTGTAAAGAATGTCAATAAAAACAATGCCTCGCATGCGGTACTCTTTGAAGCACTCGCTCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125195852|gb|EL210806.1|EL210806
EST:     AATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG                         GTCCTTCAGCGAATATTGATGGGGACAG
genomic: AATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAGgttcaatatt ... gaaatttcagGTCCTTCAGCGAATATTGATGGGGACAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
            tttgaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC